Evidence map›Paper›PMID 33313140›Full record

ArticleAnnals of translational medicine2020

ncDRMarker: a computational method for identifying non-coding RNA signatures of drug resistance based on heterogeneous network.

Haixiu Yang, Yanjun Xu, Desi Shang, Hongbo Shi, Chunlong Zhang, Qun Dong, Yizheng Zhang, Ziyi Bai, Shujun Cheng, Xia Li

Open access · diamondAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Annals of translational medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.4field-weighted citation impact, top 46% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 7 citations in OpenAlex.

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4 · The record

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5 · Who and what money

Authors and funding

10 authors at 2 institutions in 1 country.

Haixiu YangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Yanjun XuCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Desi ShangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Hongbo ShiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Chunlong ZhangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Qun DongCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Yizheng ZhangCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Ziyi BaiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Shujun ChengCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Xia LiCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
Harbin Medical University · CNChinese Academy of Medical Sciences & Peking Union Medical College · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundDrug resistance is the primary cause of failure in the treatment of cancer. Identifying signatures of chemoresistance will help to overcome this problem. Current drug resistance studies focus on protein-coding genes and ignore non-coding RNAs (ncRNAs), rendering it a challenging task to systematically identify ncRNAs involved in drug resistance.

methodsIn this study, protein-protein, miRNA-target gene, miRNA-lncRNA interactions were integrated to construct a mRNA-miRNA-lncRNA network. Then, the random walk with restart (RWR) method was extended to the network for identifying ncRNA signatures of drug resistance. The leave-one-out cross validation (LOOCV) and receiver operating characteristic curve (ROC) were used to estimate the performance of ncDRMarker. Wilcoxon rank-sum test was used to validate the identified ncRNAs in NCI-60 cancer cell lines. KEGG pathway enrichment analysis was implemented to characterize the biological function of some identified ncRNAs.

resultsWe performed this method on ten common clinical chemotherapy drugs and analyzed the results in detail. The region beneath the ROC was up to 0.881-0.951, which did not change significantly in the incomplete network, indicating the high performance and robustness of the method. Further, we confirmed the role of the identified ncRNAs in drug resistance, i.e., miR-92a-3p, a candidate chemoresistance ncRNA of tamoxifen and paclitaxel, can significantly classify cancer cell lines into sensitive or resistant to tamoxifen (or paclitaxel). We also dissected the mRNA-miRNA-lncRNA composite network and found that some hub ncRNAs, such as miR-124-3p, were involved in resistance of multiple drugs and engaged in many significant cancer-related pathways. Lastly, we have provided a ncDRMarker platform for users to identify candidate ncRNAs of drug resistance, which is available at http://bio-bigdata.hrbmu.edu.cn/ncDRMarker/index.

conclusionsOur findings suggest that ncDRMarker is an effective computational technique for prioritizing candidate ncRNAs of drug resistance. Additionally, the identified ncRNAs could be targeted to overcome drug resistance and help realize individualized treatment.

Indexed as

Drug resistanceheterogeneous networknon-coding RNA (ncRNA)

Identifiers

PMID33313140
PMCPMC7723624
OpenAlexW3089916758

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.